I would say...."sometimes". Yes, it's an issue.
Mostly "sniff test" items.
The P&L comes in like this:
Auto expenses $8144 ( this is an obvious complex problem within it's own)
Rent $4800 (does not rent a space - they mean biz use of home)
Utilities $3000 (home utilities)
Meals $18,514 (gross sales only $90,000)
Travel $8,015 (for a business that does not have a need for travel).
Payroll expense $24,000 (they mean a sole prop's owner's draw - which is not payroll and not an expense, of course)
Contract labor $18,000 (now we have to ask and educate about 1099s, for which we charge a la carte per the engagement agreement)
Etc.
So we call them on ALL of it. We do not file a shoddy schedule C. We un-shdoddy the client. We have simple canned explanations and worksheets for each issue.
As you know, most clients will become upset with the back and forth, and we don't like it either. But we explain that the IRS does not accept it this way (but the new client answers, "but I've been filing this way for years").
We are polite but very strict to make them fix these items so we can report them correctly.
I'll call them in during the off season for a "check-up" and teach them more about it. This works well because they think they have a great tax guy who teaches them, and it saves me time next tax season. If a client is struggling with QB online, we will log in and teach them some general things. It's part of the deal.
So.... yes, it happens and it's a PITA, but no more of a PITA than non-inclusive clients with the same issues.
Then there is the next argument, and that is, let's say they give me a P&L and I ask about and fix the "sniff test items". As far as I'm concerned, my responsibility ends there. If their material expense math for example is off by $10,000 - that's not my responsibility. I don't look at their bank statements, and since I'm not attesting to their P&L in any way, I don't feel I have to.
If a client is really messy, non-compliant, aggressive, or gives us grief over wanting to do it right, we immediately drop them. Doing your own books for a sole prop is not rocket science. It's a laziness and attitude problem. Adios.
If a client legitimately needs "bookkeeping services", we might take them (we have a dozen or so), or we refer them to a professional independent bookkeeper - though, we have trouble finding good ones in which to refer.